I want to have two laptops syncing to the same dropbox account. When both laptops are running and a new file is uploaded, the other laptop downloads it straight away and all is synced.

The problem is that when the laptop I am not working on is Off, and I upload a new file to dropbox with my other Laptop, then when I switch on the laptop that was off it begins indexing. It sees that online there is a newly uploaded file and on itself (the laptop) it isnt there. It then proceeds to delete it from online thinking I must have deleted it from my second computer.

How can I make it understand that it has to download missing files rather then deleting new ones?

That sounds like a bug with Dropbox. Dropbox should have enough event timeline data between the online space and the laptop to know that the file was added after the last update. Have you asked this question in the Dropbox support forums?
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hruntingFeb 13 '13 at 0:49

Maybe the clocks and timezones are not correct on these two machines.
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ahcoxFeb 10 at 18:51